Error in motif calculation

[KeremKurban]

I was running the notebook DotMotif-Search-in-Pinky100.ipynb and the following cell gives error.

motif = Motif("""
A -> B [spine_vol_um3 > 0.25]
B -> C
C -> A
""")

Output:

UnexpectedCharacters                      Traceback (most recent call last)
[<ipython-input-9-eaabd7ae9c73>](https://localhost:8080/#) in <cell line: 1>()
----> 1 motif = Motif("""
      2 A -> B [spine_vol_um3 > 0.25]
      3 B -> C
      4 C -> A
      5 """)

7 frames
[/usr/local/lib/python3.10/dist-packages/lark/parsers/xearley.py](https://localhost:8080/#) in scan(i, to_scan)
    116             if not next_set and not delayed_matches and not next_to_scan:
    117                 considered_rules = list(sorted(to_scan, key=lambda key: key.rule.origin.name))
--> 118                 raise UnexpectedCharacters(stream, i, text_line, text_column, {item.expect.name for item in to_scan},
    119                                            set(to_scan), state=frozenset(i.s for i in to_scan),
    120                                            considered_rules=considered_rules

UnexpectedCharacters: No terminal matches '_' in the current parser context, at line 2 col 14

A -> B [spine_vol_um3 > 0.25]
             ^
Expected one of: 
    * IN
    * OPERATOR
    * __ANON_5
    * __ANON_6
    * CONTAINS

Removing [spine_vol_um3 > 0.25] fixes the issue . Perhaps a recent update havent been tested for such filtering ?

[j6k4m8]

thanks for reporting — this appears to be due to a recent change to improve handling of weird attribute names; it's possible you could quote the name for now but I will push a fix to the notebook shortly!

[j6k4m8]

I've fixed the notebook linked in the readme; the correct motif is:

A -> B as AB
B -> C
C -> A

AB.spine_vol_um3 > 0.25